ObjectiveTo investigate alterations in the expression of circadian clock and Toll‐like receptor (TLR) genes in peripheral blood (PB) leukocytes of patients with Meniere's disease (MD) and vestibular migraine (VM), and determine whether these gene expressions can differentiate MD from VM.Study DesignObservational prospective study.SettingTertiary academic medical center.MethodsPB leukocytes were collected from patients diagnosed with MD and VM during recent vertigo attacks, as well as from healthy controls. The expression levels of 9 circadian clock genes and 6 TLR genes were analyzed using real‐time quantitative reverse transcriptase‐polymerase chain reaction.ResultsSixty‐nine participants were enrolled, including 28 patients with MD, 14 patients with VM, and 27 healthy controls. Both MD and VM groups showed lower expression of PER1 compared to the control group (P < .01). The VM group exhibited significantly lower expression of PER1, PER2, CRY1, BMAL1, CLOCK, and TIM compared to the MD group (all P < .001). The MD group had higher TLR9 expression than the control group, and elevated TLR4, TLR8, and TLR9 expression compared to the VM group (P < .05). In the VM group, patients with severe dizziness handicaps had significantly lower expression of PER2, CRY1, CRY2, and CK1ε compared to those with mild to moderate handicaps (P < .05).ConclusionThis study identifies distinct alterations in the circadian clock and TLR gene expression in MD and VM, suggesting potential differences in the pathogenesis of these 2 vertiginous disorders and highlighting the possibility of these gene expressions as biomarkers for differentiation.